WIP: Making suggested changes to index, setup, 1.1

Author: mgeaghan

docs/index.md

@@ -4,8 +4,8 @@ This workshop will provide you with the foundational knowledge required to run a
 
 ## Trainers
 
-- Cali Willet, Sydney Informatics Hub, University of Sydney
 - Michael Geaghan, Sydney Informatics Hub, University of Sydney
+- Cali Willet, Sydney Informatics Hub, University of Sydney
 
 ## Prerequisites
 
@@ -48,9 +48,9 @@ This workshop event and accompanying materials were developed by the Sydney Info
 
 ### Contributors
 
-- Georgie Samaha, Sydney Informatics Hub, University of Sydney
+- Michael Geaghan, Sydney Informatics Hub, University of Sydney
 - Cali Willet, Sydney Informatics Hub, University of Sydney
+- Georgie Samaha, Sydney Informatics Hub, University of Sydney
 - Chris Hakkaart, Seqera Labs
-- Michael Geaghan, Sydney Informatics Hub, University of Sydney
 
 ![](./assets/0.0_logos.png)

docs/session_1/1.1_nfcore.md

@@ -2,11 +2,11 @@
 
 !!! tip "Objectives"
 
-    - Learn about nf-core and its core features.
-    - Learn about the core features of Nextflow.
-    - Understand nf-core workflow structure.
-    - Learn Nextflow terminology.
-    - Learn about the nf-core community.
+    - Learn about nf-core and its core features
+    - Learn about the core features of Nextflow
+    - Understand nf-core workflow structure
+    - Learn Nextflow terminology
+    - Learn about the nf-core community
 
 ## 1.1.1 What is nf-core?
 
@@ -26,9 +26,9 @@ nf-core is published in Nature Biotechnology: [Nat Biotechnol 38, 276–278 (202
 
 - **Documentation**
     - nf-core workflows have extensive documentation covering installation, usage, and description of output files to ensure that you won't be left in the dark.
-- **CI Testing**
-    - Every time a change is made to the workflow code, nf-core workflows use continuous-integration testing to ensure that nothing has broken.
-- **Stable Releases**
+- **Continuous integration testing**
+    - Every time a change is made to the workflow code, nf-core workflows use continuous integration (CI) testing to ensure that nothing has broken.
+- **Stable releases**
     - nf-core workflows use GitHub releases to tag stable versions of the code and software, making workflow runs totally reproducible.
 - **Packaged software**
     - Pipeline dependencies are automatically downloaded and handled using Docker, Singularity, Conda, or other software management tools. There is no need for any software installations.
@@ -43,14 +43,14 @@ It is important to remember all nf-core workflows are **open-source** and **comm
 
 ![](../assets/1.1_nextflow.png){width=100%}
 
-Nextflow is the workflow language and engine that underlies all nf-core pipelines. It is designed around the idea that the Linux platform is the lingua franca of data science. Linux provides many simple but powerful command-line and scripting tools that, when chained together, facilitate complex data manipulations. Nextflow extends this approach, adding the ability to define complex program interactions and a high-level parallel computational environment based on the dataflow programming model.
+Nextflow is the workflow language and engine that underlies all nf-core pipelines. It is designed to provide a robust framework that lets us chain together all the command-line tools and scripts we need for our analyses into a single pipeline that is easy to execute.
 
 **Nextflow’s core features are:**
 
 - Workflow portability and reproducibility
     - Workflow logic is separated from configuration, allowing workflows to be "written once and run anywhere" - from local machines to high performance computing (HPC) clusters and the cloud.
 - Scalability through parallelisation
-    - Workflows define **processes** (individual computational tasks to run) and **channels** that define how data flows between them; this model natively takes advantage of parallelisation as datasets grow in size, allowing the same workflow code to efficiently process small and large datasets equally.
+    - Workflows define **processes** (individual computational tasks to run) and **channels** that define how data flows between them; this model natively takes advantage of parallelisation as datasets grow in size, allowing the same workflow code to seamlessly adapt to processing datasets with varying numbers of input samples with equal efficiency.
 - Flexible configuration
     - Nextflow supports defining configuration profiles and additional configuration files to override default settings and fine-tune processes for specific environments and datasets.
 - Integration of existing tools, systems, and industry standards.
@@ -61,12 +61,12 @@ Because of these features, Nextflow has become one of the most prevalent workflo
 
 In today's workshop, we will be focusing on the configurability of nf-core pipelines, and so won't be further exploring the inner workings of Nextflow. If you would like more information about how Nextflow works and how to write your own pipelines, you can see our [Nextflow for Life Sciences training material](https://sydney-informatics-hub.github.io/hello-nextflow-2025/), as well as the [Nextflow documentation website](https://docs.seqera.io/nextflow).
 
-!!! abstract Poll 1.1.2"
+!!! abstract "Poll 1.1.2"
 
     One of Nextflow's strengths is that it can be run on many different platforms and can run scripts written in lots of programming languages. Let us know:
 
     1. What platform do you run your bioinformatics workflows on? A desktop or laptop? An institutional HPC?
-    2. What language to you prefer to write your scripts in? Bash? Python? R? Perl?
+    2. What language do you prefer to write your scripts in? Bash? Python? R? Perl? Something else?
 
 ## 1.1.3 nf-core workflow structure
 
@@ -116,5 +116,6 @@ Upcoming events are listed on the [nf-core event page](https://nf-co.re/events)
 
 !!! note "Key points"
 
-    - nf-core is a community effort to collect a curated set of analysis workflows built using Nextflow.
-    - Nextflow is a workflow management engine and coding language that makes it easy to write data-intensive computational workflows.
+    - nf-core is a community effort to collect a curated set of analysis workflows built using Nextflow
+    - Nextflow is a workflow management engine and coding language for data-intensive computational workflows
+    - nf-core workflows are written in Nextflow, combining a series of modules and subworkflows into a main workflow

docs/setup.md

@@ -54,7 +54,7 @@ Having successfully logged in, you should see a small blue or green box in the b
 
 ### Install extensions on the remote machine
 
-We will now install some helpful VS Code extensions to help with Nextflow syntax highlighting and viewing reports on the remote machine:
+We will now install some helpful VS Code extensions. The "Nextflow" extension adds Nextflow-specific syntax highlighting. The "Live Server" extension enables us to view HTML reports on the remote machine without having to download them first.
 
 1. Ensure you are still connected to the VM as above.
 2. Click on the extensions button (four blocks) on the left side bar.